A Fresh Start
by AikoTsuki
Summary: Perry's whole life is turned upside-down when Linda's niece, Alexis Pantome, decides to become a part of their family. COMPLETE
1. Chapter 1

**Okay, so I changed chapter 1.**

**Disclaimer: I don't own Phineas and Ferb**

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Adjustment Arc: Prelude

_Perry_

Major Monogram finally gave me a day off from fighting Doofenshmirtz. The OWCA formed an alliance with a group called Lithium, and I was sent to meet with Lithium's boss and head agent- Alexis Phantome and Violet, respectively.

I followed Monogram's instructions, opening a secret entrance in the lobby of a high-rise apartment building near DEI. A panel in the wall slid open, and I stepped into a glass elevator that sent me flying underground.

I stepped out. A teenage boy rode up on a skateboard. He was maybe a bit younger than Candace, with longish wavy blond hair and blue eyes. He extended his hand, and helped me onto his board. "I'm Xander. Are you Agent P?"

I nodded. He led me through dimly lit tunnels to the main conference room. I stepped off, and he sped down the hallway. The door was slightly ajar. I walked inside and took a seat at the long, professional-looking table

There were only two people inside. There was a young woman who was maybe in her early 20's, with waist-length dark brown hair. Sitting next to her was a girl about Vanessa's age, with hip-length black hair and dark brown eyes.

"Welcome, Agent P," the woman said. "I'm Alexis, and this is Violet." Violet nodded.

Alexis leaned across the table. "Do you know why Major Monogram sent _you _here, specifically?"

I shrugged.

"Monogram told me that you've had quite a few close calls when it comes to your family finding out about your work, correct?"

I nodded.

"The thing is, with this new alliance, if your family finds out, there is another outcome besides you leaving or them having their memories erased."

I raised a nonexistent eyebrow.

"Part of the terms for our alliance is that if any Lithium agent discovers their pet works for the OWCA, then the OWCA has to allow their agent to stay with their family. If your family learns about your secret identity, you can stay with them if at least one person agrees to work for Lithium."


	2. Adjustment Arc: First Contact

**Okay, now time for Chpater 2!**

**Disclaimer: I don't own Phineas and Pherb, but I DO own Lithium.**

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**Adjustment Arc: First Contact**

_Phineas_

Mom was making dinner when the doorbell rang. Candace opened the door. Her eyes widened.

"Alex?!"

"Candace?!"

Candace hugged the stranger, a woman in her early twenties. Ferb raised an eyebrow. I shrugged.

Candace looked at Alex's companion, a boy about Ferb's age. "Jason?"

"Hey, Candy."

Ferb and I were clueless. "Mom! Cousin Alex and Jason are here!"

"What?!"

Mom walked into the living room. "What are you two doing here? Does Bonnie know?"

"Mom's dead, Aunt Linda," Alex said. "She died a few months ago in a car crash."

Mom fell onto the couch. "She's…dead?" she whispered.

"Wait a second, what's going on?" I asked.

Mom turned to me and Ferb. "These are your cousins, Alexis and Jason Phantome. Their mother- my older sister- and I haven't spoken to each other since you were born, Phineas." She turned to Alex. "I thought you lived in San Francisco. What are you doing here?"

Alex shrugged. We moved here for some peace and quiet, and I decided to see if you were still living in the suburbs."

Alex's phone went off. She looked at it, then face-palmed. "How could I forget _that?"_

"Forget what?"

"I agreed to give a speech at a week-long Women in Engineering Conference in New York. My flight leaves in two hours and I haven't packed or found someone Jason can stay with or-"

Mom put her hand on Alex's shoulder. "He can stay with us. Why don't I go to your house with you and help you and Jason pack?"

_Alex_

I opened my laptop after the plane took off.

"I can't believe you forgot," Kira said through video-chat. "I mean, sure, you forget meetings, appointments, vacations, but a week-long conference?"

I rolled my eyes. "Aw, be quiet." I heard shouts and crashes in the background, along with an explosion. "What are you doing?"

"Xander and I are training. It's the obstacle course."

"I see. Don't kill that boy, we need him. Oh, and you're in charge until I get back."


	3. Adjustment Arc: Discovery

**Okay, now things are going to get interesting. **

**TheEpicDuck123: Thanks for reading. I hope you like where I'm going to go with this.**

**Disclaimer: I don't own Phineas and Pherb. **

**Note: I changed Violet's name to Kira. Just saying this to eliminate any confusion**

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**Adjustment Arc: Discovery**

_Phineas_

We decided to create a spy camera the next morning. A few minutes later, Jason looked around and asked, "Where'd Perry go?"

"I don't know. It seems like every day, Perry just…disappears."

Jason grinned. "I have an idea- let's use the Spy-Cam to see what Perry's up to."

_Perry_

I burst into DEI. As usual, Dr. D's trap closed around me.

"Perry the Platypus, I have created the ultimate weapon for taking over the Tri-State area- the Slaveinator!" Dr. D shouted, wheeling his device onto the balcony. "It turns anyone it zaps into mindless slaves, obedient to me alone!"

I broke free and shoved Dr. D away from his invention, when the Inator, Dr. D, and I were caught in a spaceship's tractor beam.

_Jason_

The Spy-Cam's connection blacked out.

"We have to rescue Perry," Phineas said.

"Why? He lied to us," Buford argued.

"So what?! He's still a friend!"

I stood. "I know who took him, and someone who can help us get Perry back."

"Who?"

"Perry was kidnapped by a race of aliens called Konaks, who are trying to conquer Earth. My sister runs a secret Organizations called Lithium, who fight the Konaks. There's an entrance to their headquarters a few blocks away."

"Let's go."

We walked to a nearby laundromat. I uncovered a part of one of the washers, revealing a scanner I pressed my hand to. The washer split, uncovering the entrance to a metal chute.

"Well, go on."

Phineas jumped in, followed by Ferb, Isabella, Buford, and Baljeet. I went last, the opening sliding closed behind me.

We fell into a cavernous room. Kira and Xander were in the middle, fighting a horde of ninja-bots. _What is it with her crazy training exercises? _I walked to a control panel on the wall and turned off the robots.

Kira brushed a dark lock out of her eyes. "What was that for?" she demanded.

"Agent P, Dr. D, and one of his Inators were just captured by the Konaks."


	4. Adjusment Arc: Transformation

**Disclaimer: I don't own Phineas and Pherb.**

**Warning: Incredibly dark chapter ahead.**

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**Adjustment Arc: Transformation**

_Kira_

My mouth dropped open. "What?"

Jason and the others explained the situation.

"I stuck a remote-controlled camera on Agent P's fedora," Xander said. "Let's use it to see what's going on."

_Perry_

I opened my eyes. I was strapped to a metal examination table, floodlights burning my eyes. A blurry figure towered over me. It looked like a giant rat.

"Tell me how to use the device you came with," the creature demanded. I glared at him.

"I forgot, you cannot speak," the creature said, its voice sounding like a low-pitched screech. "This will help." I felt the sting of a needle being injected into me.

Indescribable pain seared through my body. I twitched and writhed in pain, leather restraints tearing into my body. Eventually, I blacked out.

Later, I opened my eyes. "Look at your body," the creature ordered.

I turned my head. A long, pale-skinned _human _arm replaced my platypus one. I looked down. A _human _torso, human legs, human feet.

"What did you do to me?" I whispered, my voice hoarse.

"I gave you a voice. Now answer my question."

"I don't know how to use the Slaveinator," I said. "I didn't create it. Even if I knew how to use it, I'd still never tell you."

The creature slapped me. I winced. It turned. "Then I suppose I'll have to speak to your companion, yes?"

_Xander_

We watched the Konak turn to Dr. D, who was in chains. "Will you answer our question?" the alien asked.

"Why do you want it?" Dr. D asked.

"To take over the world, of course, starting with Danville."

Dr. D glared defiantly at the Konak. "I'll _never_ tell you," he growled.

"Perhaps this will change your mind."

The Konak picked up a syringe from a nearby metal tray and stabbed it into the man's arm. He howled in pain, body trembling, sweat pouring from his body. He crumpled to the floor. We watched as his body started to shrink, Dr. D becoming a teenager.

When he finally woke up, he noticed that his clothes were a bit too big for him. "What did you do to me?" he demanded, voice cracking at the end.

"I made you about twenty years younger," the Konak replied. "Will you cooperate, or do I need to try something else?"

"My answer is still no."

The Konak's tail swung, smashing the camera to bits.

_Perry_

Another creature walked into the room. "The prisoners are wanted on the bridge."

My restraints were undone. I sat up, rubbing my wrists. A teenage Doofenshmirtz was unchained. He wrapped his lab coat around my shoulders, as I wasn't wearing any clothes.

"Thanks."

The two of us were shackled and led through the halls of what seemed to be a massive spaceship. I shivered. It was freezing onboard.

We were led into a huge spherical room, windows providing an excellent view of space, the moon, Earth. I glanced longingly at the blue-and-green planet. I wondered if I'd ever get home, ever see my family again.

A small gathering of the rat-creatures (who I now assumed were aliens) were in the room. The largest one stepped forward. "I am General Liev, commander of the Konak army," the creature said. "I understand that you are unwilling to comply with our requests."

Liev turned. "Heinz Doofenshmirtz, you have spent the past few years of your life obsessed with taking over the Tri-State area, correct?"

Doofenshmirtz nodded, scowling at the alien. My body started to feel hot.

"Why not help us take over the world, and we give you control of the Tri-State area?" Liev suggested.

"Never," Doofenshmirtz said defiantly. My body started shaking.

A smaller Konak ran up to the General. "Sir, we figured out how to use the device!"

Liev turned to us, grinning. "It seems you are no longer needed."

I collapsed.

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**Like I said, dark. I decided to give Dr. D some sprit, which helps the story.**

**Please read and review!**


	5. Adjustment Arc: Recovery

**Yay! People like this story! **

**I'll be dividing it into three "Arcs"- Adjustment, Preperation, and Secrets. The major battle takes place in the Secrets Arc, but most of the inportant informationm is in the Preperation Arc.**

**Disclaimer: while I ****_do _****own Lithium, I do NOT own Phineas and Ferb**

**Warning: epicly long chapter ahead!**

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**Adjustment Arc: Recovery**

_Kira_

I lead the others to the fighter hangar, explaining things along the way.

"The mother ship is hidden behind the moon. Konak transformations cause a potentially fatal reaction, so if we don't get to Perry in time, he might die."

Lithium technology comes from an alien race known as the Gullrays. Their fighter ships look like giant arrowheads with a huge gyrating Plexiglas orb at the tip containing the pilot and passenger seats. We all loaded onto my fighter, which I piloted.

_Heinz_

Perry fell to the floor.

"Perry!" I shouted, cradling the platypus-turned-boy in my arms.

"Sir! We have a Lithium fighter approaching the ship at top speed!" an underling announced.

"Scramble the pilots! Shoot it down!" General Liev ordered. He turned to our captor. "Kill the inventor, as slowly and painfully as possible."

"What about the boy?"

Liev looked at the small figure in my arms. "He's nearly dead. Make Doofenshmirtz watch him die."

_Kira_

Isabella looked at the radar. "We have a bunch of enemy ships approaching fast!"

Xander leaned over. "There's too many, Kira. We can't take them."

"Why don't we try Configuration Beta47A?"

"What's that?" Baljeet asked.

"Basically, we create mini-fighter-orbs for everyone to use while one person stays with the ship."

"Let's try it."

_10 minutes later…_

"Phineas, your left!"

"Buford, help me shake these guys off my tail!"

Die, aliens! DIEDIEDIE!"

"Take that, you jerks!"

"Only one left!"

BOOM!

"We did it!"

_Heinz_

They led us away, with me carrying Perry. I managed to get a good look at Perry's new face- his skin was incredibly pale, and was maybe ten or eleven years old. Sweat plastered his spikey blond hair to his forehead.

I felt incredibly guilty. It was my fault Perry was like this. Sure, he was my nemesis, but I didn't want him to _die. _

Our captor led us to a lab/torture chamber-type room. My hands were chained to the ceiling, and my feet were chained to the floor. I was suspended in mid-air, with Perry in full view.

Perry had been laid on a metal examination table. He was unrestrained, being almost too weak to move.

Our captor pulled out what looked like a cat-of-nine-tails made out of steel cable, glowing and crackling with electricity. He approached me, grinning evilly.

THWAP! He whipped my torso.

THWAP!

THWAP! He began doing the same to my back.

THWAP!

THWAP! I realized my chains were loose enough to slip out of. _The second he turns around-_

_Kira_

We managed to slip into the Konak ship unnoticed. I passed photon guns and cartridges to everyone in the group.

"Here's the plan- one person goes and rescues Perry and Dr. D, while the rest of us go destroy the Slaveinator," I said.

"Why don't you go?" Xander suggested. "We can handle the big guys."

I nodded.

"Use a disguise."

I smiled. I got onto my knees, quietly shape-shifting into a huge wolf. Xander tied a dress around my neck for me to wear when I changed back.

"What happens if one of us has to leave before the other gets back?" Phineas asked. Xander pressed a button on the underside of the ship, producing a double.

"Let's go."

_Heinz_

The alien finally turned around. I slid out of my bonds, silently dropping to the ground. I started to make my way towards Perry when the Konak spotted me.

"Hey!" he shouted, running after me.

I scrambled under Perry's table. The Konak crashed into it, trying to grab me. Perry moaned in pain.

I was trapped. I needed something to distract the alien. I noticed a scalpel on the floor. I jabbed it into the Konak's paw. He staggered backwards, howling in pain.

I crawled out, scanning the room for a better hiding place. The alien chased me, screaming what were probably alien profanities. I kept him away by weaving through tables, dashing through narrow spaces, knocking things off tables.

I heard a low growl. I turned as a wolf leapt onto the Konak, biting the alien's shoulder and holding on tight. The Konak screamed, trying to shake the animal off.

I saw a ray gun-type device on a nearby table. I picked it up and fired it, an intense beam of light hitting the Konak in the head. He fell, smoke coming from his forehead where the beam hit.

The wolf looked at me, changing into a dark-haired teenage girl. She quickly untied the dress around her neck and pulled it over her head.

She picked up another ray gun. "Grab Perry. Let's get out of here."

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**Like I said, long.**

**Perry: I didn't realize Dr. D could actually defend himslef.**

**Kira: I helped!**

**Heinz: I'm not useless, unlike ****_some _****people.**

**Perry: Hey!**

**ellahikair15: be nice, everyone. Phineas-**

**Phineas: Please read and review!**


	6. Adjustment Arc: Escape

**Okay, now we're getting more people involved!**

**I will apologize ahead of time, the next few chapters are going to get pretty long.**

**Phineas: Ellahikari15 does not own Phineas and Ferb.**

**Xander: But she ****_does _****own me!**

**Kira: And the rest of Lithium.**

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**Adjustment Arc: Escape**

_Kira_

I led Dr. D and Perry back to our ship. The halls were strangely deserted. What was going on?

I tapped my communication watch. "I have Perry and Dr. D. How are things on your end?"

"Not good," Xander said. "The General took off with the Slaveinator before we got here. He connected it to a bunch of phasers. Get hit and you become Liev's slave."

"That _is _bad. Do you know where he took the Slaveinator?"

"DEI."

We froze. I calmly said, "Okay. You guys get back to Danville, and we'll meet up at DEI."

_Xander_

We started to leave the ship's bridge when a laser cage sprung up, trapping us.

Sargent Lillk, Liev's second-in-command, stepped out of the shadows. "I knew someone would come for the device." He leaned close, face inches from mine. He grinned. "You think you're a hero? You're not. Heroes don't exist."

_Heinz_

The ride back to Earth was quiet until an SOS message from Monobrow came through.

"Need help…too many…taking over…AARGH!"

The connection died. The girl looked at me, a silent concern passing between us.

A few minutes later, the awkward silence was killing me. "Hey, um, what's your name?" I asked.

"Kira."

We flew over Danville. The city was in shambles. Buildings were burning and destroyed, abandoned cars littered the chaotic streets, the entire population was in pure pandemonium. The military had moved in, but they were no match for the Konaks. We were fighting a losing battle.

A large hole opened in an empty field. We sank through, landing in a spaceship hangar.

About 50 people were waiting for us. Kira stepped out and was swarmed by the nervous, noisy crowd.

"Quiet!" Kira shouted. "I'm going to change. Dr. Monroe?"

"Yes?"

"Agent P's been through a Konak transformation. He needs immediate medical attention."

"Yes, ma'am." A man in a lab coat carried Perry away.

"Everyone else, we're having a planning meeting in 10 minutes!"

_Candace_

I walked through the underground base, searching for my brothers. "Phineas? Ferb? I know you're here, please come out."

A boy and a girl ran into me. "Get to your station!" the girl ordered.

"Station? What is this place? I'm looking for my brothers."

"Are you Phineas and Ferb's sister?"

I nodded.

"They're helping fight an alien invasion."

"I want to help."

"Come with me."

_Xander_

Lilk's men led us to a holding cell. The second the aliens left, Phineas and Ferb started working on busting us out. We were free in 15 minutes.

"Come on," I said, "before Earth becomes slave to these alien rats."

_Candace_

Kira, the girl, led us through dimly-lit halls. "Heinz and I need to change, and there's _no way _you'll be able to fight in that, so that's what we're taking care of first."

Kira opened a door, revealing a department-store-sized selection of clothes. She led us through the racks, picking out clothes for everyone.

Kira held up an outfit. "GO try this on, Heinz." He returned a minute later, wearing a black shirt, white pants, white vest, and black shoes. Kira was busy finding clothes for me.

"What about these?" she asked, holding up a white cardigan, green cami with black lace, black pants, and black boots.

"Perfect."

I returned to find Kira in _her _outfit- a purple áo ba bá, black pants, and purple and black combat boots.

"Let's go."

_Xander_

Unlike Kira, we had to battle our way back to the ship. I'm surprised we all made it back in one piece.

"Let's go meet up with Kira."

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**Wow. That was long. Now Candace is involved!**

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	7. Adjustment Arc: Conflict

**Okay, things are getting close to this arc's climax! Maybe another chapter or two and I can start on the second story Arc. By the way, I'm changing the next arc to being the Secrets Arc. **

**Disclaimer: I don't own Phineas and Ferb**

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**Adjustment Arc: Conflict**

_Kira_

We walked to the conference room, where every team leader was waiting. A holographic map of Danville was on the table.

"Okay everyone, it looks like the Konaks are officially invading Earth," I said. "They're using Dr. D's Slavinator, which is connected to a bunch of phasers. Those who are hit become the Konaks' slaves. They most likely have other weapons, so be careful."

I turned to the map. "Alpha and Xi teams, you handle the North side. Beta and Chi teams, take care of the South end. Theta and Omega teams, go to the West side. Gamma and Delta teams, go deal with the East End. Zeta and Iota, the suburbs. Epsilon and Sigma, the outskirts. Candace, Heinz, and I will deal with the situation at DEI. Okay, let's move out!"

Dr. Monroe approached us. "Kira, I was analyzing Doofensmirtz's bio-feedback, and it looks like he's undergoing a Reaction."

"Impossible."

"We have to be sure."

"I'll bring him to your lab."

_Candace_

Kira led us to Dr. Monroe's lab. "What's a Reaction?" Heinz asked.

"What Perry went through after the transformation."

Dr. Monroe was waiting next to an MRI-type machine. "Please take off your shirt and lay down," he instructed. After Heinz was inside the machine, the doctor sat down at his computer. A few minutes later he looked up and said, "He _is _undergoing a Reactions, but it's faster than anything I've ever seen. I'm surprised he hasn't felt anything yet."

"Can you treat it?" Kira asked.

"I'm not sure. We could try Delta, but-"

"Do it."

We pulled Heinz out of the machine. The doctor pulled out a needle filled with a strange red liquid, which he injected into the teen's arm. He passed out a few seconds later.

_Heinz_

I awoke to someone shaking me. "Heinz! Heinz!"

I opened my eyes. "Candace?"

Candace squeezed me. "You're okay! You were out for over fifteen minutes!"

Kira and Dr. Monroe were standing off to the side.

"What happened?" I asked.

Kira helped me up and led me to a full-length mirror.

I was about Candace's age, but slightly more muscular, like someone who actually worked out. My hair was a bit longer and straighter, and my hair and eyes were a couple shades darker than before. All in all, not much had changed.

"So what?" I asked.

"Turn around."

I obeyed. A pair of snow-white wings had sprouted from my shoulder blades.

"What did you do to me?!"

"Your body was destroying itself," Kira said simply. "So we stopped it."

"_The wings."_

"We used Delta, an experimental drug used to give people superhuman strength, speed, and abilities. It only works on hybrids, so there was a bit of avian DNA mixed in," the doctor explained.

A few minutes later we were preparing to storm DEI. Kira had cut slits in my shirt for my wings. She then handed me and Candace belts with pouches for 10…things. They looked like blacklight tubes, only they were small and glowing white. She also handed us ray guns.

"These are photon guns," Kira explained. "They use cartridges, which are good for ten shots."

"How do we change the cartridges?"

Kira opened the bottom of the grip. One of the tubes slid out. She popped it back in place. There was a slit in the grip, which glowed white. She pointed to it and said, "Change the cartridge when it turns yellow."

We put on the belts and slid the photon guns into their holsters. Kira led us to the garage, which held all sorts of vehicles, from trucks to ATVs to tanks. Kira grabbed a red motorcycle, and tossed us our helmets. "I'll drive," she said. "Candace, sit behind me and cover our front and tight. Heinz, sit behind Candace and cover the left and back."

_Candace_

We zoomed into the partly destroyed city. Large parts were deserted, and we had to weave through abandoned and crashed cars.

I spotted Jeremy and Stacy, who were fighting off a swarm of…zombies? They certainly had the blank, lifeless expression and creepy groan correct.

"The Slaveinator did this," Kira whispered. She pulled out her gun.

"Don't hurt them!" I cried.

"I won't." A beam shot through the crowd, burning a hole in a nearby wall. The zombies fled. Jeremy and Stacy looked in our direction.

"We're going to go stop the zombie problem!" I said.

"Can we come?" Stacy asked. Kira nodded. She pulled out a small device and attached it to an abandoned moped, which roared to life.

"Hop on."

"Kira then handed Jeremy and Stacy photon guns and cartridges, while I quickly explained how to use them.

We took off for DEI.

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**Please read and review!**


	8. Adjustment Arc: Reunion

**Okay, things are about to fall in place. One more chapter before the end of the Adjustment Arc!**

**Disclaimer: I don't own Phineas and Ferb. Disney does.**

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**Adjustment Arc: Reunion**

_Heinz_

We discovered that the Konaks were holding and NBC camera crew hostage and were forcing them to film what was happening. Kira told us a group of humans called Black Rose worked for the Konaks, and they'd target us and our families if they knew who we were. So we _borrowed _some hats and sunglasses to hide our faces.

The entrance to DEI was guarded by two Konaks.

"We need a distraction," Kira hissed. We were hiding behind an overturned semi.

"I'll go," Stacy offered. Kira handed her a small, metallic box.

"It'll protect you from the Slaveinator," she explained.

Stacy ran out into the open. "Hey aliens!" she shouted. "Here's one human you didn't zombify!"

"Hey!"

Stacy took off, with the guards following close behind. The rest of us snuck into the building.

_Kira_

Seeing as the elevators weren't working, we had to take the long way to the top, involving a lot of sneaking around Konak soldiers who were patrolling the building.

We finally reached the top floor. I saw General Liev at the Slaveinator's controls, surrounded by a dozen soldiers. Four soldiers were standing by the camera crew. Numerous soldiers were scattered throughout the floor. We were severely outnumbered.

I noticed a figure propped against the wall. My eyes narrowed, then widened.

They were holding Alex Phantome, head of Lithium, hostage.

_Xander_

We hovered over DEI. "I found Kira!" Phineas announced.

"Isabella, turn off the cloaking device!"

"The ship is now perfectly visible!"

"Buford, Baljeet, stay with the ship in case we need backup. Everyone else, we're going down!"

A door in the ship's floor opened. We stepped off the edge, hover boarding to the ground. Kira and her crew burst out of hiding.

Phineas' eyes widened. "Candace?!"

"Phineas!"

A photon blast pierced the air. "Sorry to break up the teary reunion," Liev said, "but you're all about to die."

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**What will happen next? Please read and review!**


	9. Adjustment Arc: Finale

**Here's the last chapter of the Adjustment Arc! The battle ends here, but not the story!**

**Disclaimer: I do't own Phineas and Ferb.**

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**Adjustment Arc: Finale**

_Kira_

"You're all about to die."

Within seconds we were surrounded and defeated, our hands tied behind our backs.

"Why don't we start with your boss?" General Liev dragged Alex to the center of the room, knife playing with her throat. "Such a shame to kill a babe like this one."

"May I speak to Kira before I die?" Liev nodded. I was shoved foreward.

"You have to get out of this," Alex hissed. "I named _you _as my successor."

I nodded. Live separated us. "Time to die." The knife sank into Alex's throat, and she breathed one last time before falling to the floor. Liev turned to me. "Your turn, little miss."

"I don't think so." At that moment, Xander and I broke free of our bonds. Xander set to fighting the Konaks and freeing the others, while I dealt with Liev and the Slaveinator. If I could just destroy that device, Danville would be free and the Konaks would be forced to retreat.

_Xander_

A few seconds after I freed the others, Stacy crashed in on a hoverboard. She instantly jumped into the fray. I found myself fighting back –to-back with her a few minutes later.

"So, what'd I miss?"

"Not much. We just got captured, and Lithium's boss was just killed."

"So I missed all the good stuff?"

"Nah. This is the fun part."

"Never thought I'd be fighting aliens alongside such a hot guy."

I blushed.

I saw Kira almost about to fall off the edge of the balcony. She shoved Liev out of the way, then looked at the Slaveinator. A huge electrical explosion emanated from Heinz. Kira grinned.

"Heinz, get over here!" Kira shouted.

_Heinz_

I was fighting for my life, almost running out of shots faster than I could reload.

A Konak slapped my photon gun out of my hands. I grabbed the alien's tail. I felt a surge of electricity flow through me and into the creature. It was amazing. I actually laughed, the euphoria was so incredible.

There was a huge explosion. When the smoke cleared, the alien was dead. I looked at my hands. _Did I do that?_

_Kira_

I realized freezing the Slaveinator would merely stop the commands, not destroy it. I needed something to fry the system. Suddenly, Heinz created a huge electrical explosion. I grinned. _Perfect._

"Heinz, get over here!"

Heinz was at my side in a matter of minutes. Xander and Stacy were engaging Liev in and all-out, attention-consuming firefight.

"We need you to fry the Slaveinator's controls," I explained. "I need you to put your hands on the keypad and exert as much electricity as possible."

"How?"

"Imagine all of the electrical impulses in your body coming together and exiting through your fingertips."

Heinz closed his eyes and focused. The air crackled and popped around us as the wind started to blow through DEI. There was an immense flash and the Slaveinator fizzled out, a charred wreck.

Liev realized his plans for world domination just slipped through is fingers. "Retreat!" A swarm of Konak fighters picked up their soldiers and flew away.

"Fall back!" I shouted. We grabbed hover boards scattered around the floor and made our way back to HQ.

"Why are we leaving?" Candace asked as we flew off. "Shouldn't we stay and help clean up?"

"Cleanup will take anywhere from a few days to a few weeks," I explained. "If we stayed NBC would get a close-up of our faces."

_Candace_

We watched the news report. No one knew who we were, but Heinz Doofenshmirtz was declared dead, thanks to the General's statement. _("The owner of this apartment is already dead. I made sure of it.")_

My mom, Buford's, Baljeet's, and Isabella's parents didn't want the younger kids involved in the resistance. They had their memories of the day erased and were sent home.

Kira returned from dropping off the kids. Heinz, Stacy, Jeremy and I were In Dr. Monroe's lab. Perry was still unconscious.

Kira leaned against a counter. "So, what do all of you want to do?"

"Aren't you going to call our parents?" Jeremy asked.

"People over 14 are allowed to make their own decisions."

"Well, I'm joining Lithium," I said.

"Me too," Stacy said. "I had fun today."

"I'm with Candace," Jeremy said. I blushed.

"I feel guilty about what happened," Heinz said. "I'm giving up evil and joining Lithium."

"You'll need a new name," Kira said.

"How about Sebastian?" I suggested.

"That works."

Kira smiled. "The four of you are _amazing _fighters, but you still have a lot to learn. Why don't we get started?"

* * *

**Whew! Glad that's finally over. Now onto part 2: the Secrets Arc!**

**Please read and review!**


	10. Secrets Arc: Awakening

**Here comes the second Arc!**

**I don't own Phineas and Ferb**

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**Secrets Arc: Awakening**

_Candace_

I walked into HQ the next morning, having managed to slip away after my brothers decided on what they were gong to do that day.

Everyone else was already there. Heinz- I mean, _Sebastian _had spent the night at HQ. Perry would be waking up soon. We walked over to Monroe's lab, where Perry was sleeping.

We heard a blood-chilling scream.

_Sebastian_

We burst into Dr. Monroe's lab. Kira was cradling a sobbing Perry on his bed.

"What happened?"

"He had a nightmare," Kira explained. "Shhh. It's okay; it's just a bad dream. Everything's going to be okay," she murmured in the boy's ear.

His sobs quieted. He looked at us. "What happened while I was asleep?"

_Perry_

Kira and the others explained what happened.

"Will they come back?"

Kira and Xander nodded.

"I wand to help stop them." I started coughing.

"Careful," Kira warned, "you're still recovering."

Kira looked up. "That reminds me- we still need to make you all official Lithium agents."

_Candace_

"What do you mean, _official?" _I asked.

"All Lithium agents have a microchip embedded in the back of their neck," Xander explained. "It's a tracking device, but it also protects the agent from any mind-control devices."

"Wish I had one of those yesterday," Stacy snorted.

Dr. Monroe pulled out a staple gun-type machine. He pressed it to the back of my neck. I heard a click, felt a sting, and it was done. I was now a real Lithium agent.

* * *

**Ha! Done!**

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	11. Secrets Arc: Acclimatization

**Sorry it's been a while. I lost my inspiration. I came up with a few P&F Character-OC pairings, see if you can figure them out!**

**I don't own Phineas and Ferb.**

* * *

**Secrets Arc: Acclimatization**

**_Kira_**

It had only been two days since Alex died, and I was still trying to process all these changes.

_I can't believe _I'm _the boss now, _I thought as I walked out of the shower.

Perry decided to join Lithium. He also decided to change his name to Ryder, which I thought was a pretty cool name.

Raella was in charge handling the agents' living arrangements, which meant she would be finding a place for Ryder and Sebastian to stay. I met with her after breakfast.

"They're what?!" I nearly shrieked.

Raella nodded. "They're staying with you."

"What about the no 'boy+girl in same apartment' rule?"

"Technically, it'll be 2boys+girl in same apartment, so it's okay. You're the only person in a two-bedroom apartment. You can share."

I sighed. "Fine."

* * *

**_Candace_**

"I'm going to the mall with Stacy today," I said at breakfast.

"Have fun!" everyone called.

Stacy, Kira, and I were dragging Sebastian and Ryder to the mall to get stuff for their new room, and they _desperately _needed some new clothes.

We met up at the food court. "Why don't we shop for clothes last," Stacy suggested, "since it'll take the longest?"

_Three hours later_

"Try this on, Ryder!"

Kira helped Ryder into a black tee under a green shirt and jeans.

"Get over here, Sebastian!"

Stacy and I convinced Sebastian to try on a grey tee under a white t-shirt with black runic designs and black pants.

"Our turn!" Stacy shouted.

We forced the boy to witness a fashion show as we went in and out of outfits, each settling on the outfit we liked the most.

I got a purple shirt with white raglan sleeves and jeans. I was trying to look tomboyish, to get less catcalls from the guys at HQ.

Stacy, on the other hand, went for a pink boat neck shirt, white cami, and a brown skirt. Very cute.

Kira had got a similar outfit, although the shirt was white with turquoise sleeves.

"Let's accessorize," I said.

Ryder got a pair of black fingerless gloves and boots. Sebastian got a black newsboy cap and black shoes. I got a purple cap and sneakers, and Stacy got a pink purse and brown penny loafers. Kira simply bought a pair of sneakers.

_**Stacy**_

We went back to Kira's apartment. Thankfully, Raella's team had already set up the boys' new room.

Xander was in the lobby when we arrived. "Did you girls go shopping?"

We nodded.

"Why don't I help you carry your stuff upstairs?" he suggested.

Kira lived on the tenth floor of a 15-story apartment building. I walked behind Xander and couldn't help but notice the confident way he carried himself, or his rippling muscles. _He's probably on the football team._

Kira went inside first. She set down her bags and plopped onto the couch.

Sebastian arrived last. He tripped over a shopping bag, landing on top of Kira. Their eyes met for a moment, the Kira shoved him off, blushing.

_**Sebastian**_

Three weeks went by. I started high school, and Ryder started middle school with Phineas and his friends.

Kira was head of the student body, captain of the girls' soccer team, queen of the tennis court. She was an amazing fighter, and a great teacher. She also happened to be a shape shifter with a supermodel figure.

I threw myself onto my bed. Ryder was on the bed opposite mine, doing his homework.

"I think I have a crush on Kira."

Ryder snorted. "Like that'll ever work out."

I threw a pillow at his face.

"Hey!"

* * *

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	12. Secrets Arc: Defense

**I hope some of you figured out what my pairings are!**

**I don't own Phineas and Ferb**

* * *

**Secrets Arc: Defense**

_Sebastian_

Kira, Xander and I attended Cascade High, a private school with a 56% Lithium agent student body. Candace, Jeremy, and Stacy transferred to Cascade at the beginning of the year.

Cascade had school uniforms for all of their students, which Stacy alternately liked and hated, depending on the day. Today, she loved the uniform.

"I mean, cream and lavender go together perfectly," she was saying (the girls wore cream vests and lavender skirts). Kira rolled her eyes.

"Are you guys busy this weekend?" she asked. "Because I'm supposed to go to the moon base on Saturday."

"We have a moon base?" I asked.

"You didn't know?"

We all shook our heads.

"Oh, well, it's mostly for shipbuilding and interplanetary negotiations."

_Candace_

We arrived at the moon base on Saturday morning. It looked like a tall, thin tower on top of a giant metal pod.

We met with Christopher, who was head of the base.

"What's wrong?" Kira asked.

"We intercepted a communication between General Liev and the Konak home world. He's requesting reinforcements."

"He's getting serious," Kira noted. "Do we have the materials to implement Plan Lambda347?"

"No."

Kira sighed. "I'll contact Marshal Xerxes." She turned to us. "Are you coming?"

* * *

**Please read and review!  
**


	13. Secrets Arc: Past

**Spoiler alert! Major insight into Kira's past is about to be revealed!**

**I don't own Phineas and Ferb**

* * *

**Secrets Arc: Past**

_Stacy_

The conference room was at the top of the tower. The walls had huge windows, giving a 360 degree view of the surrounding area- the dark side of the moon. There was a long white table facing a screen. Kira aimed a remote it, and a Gullray appeared on screen.

Gullrays look a lot like humans, but their skin is pale, translucent, with a blueish tinge. They have a long, barbed tail, and their hair is blue, and their eyes are purple. Gullrays are the only shape-shifting alien race in existence. This one was a male.

"Are you the new head of Lithium?" he demanded. Kira nodded.

"Marshal, it seems that the Konaks are getting serious about invading Earth. We need to prepare for a full-on invasion."

"What do you need?"

"Plans, mostly. For command ships and ferries, along with the materials to make them. We'll also need materials to make new fight suits."

"We have fight suits?" I asked. Candace shushed me.

The Marshal nodded. "I will help you, but on one condition."

"What's that?" Kira asked.

"Sixteen years ago, a human woman and I decided to have a child together. Two twin girls were born, and were taken by the Konaks. They would be the only human shape-shifters on the planet. I want you to help me find them."

"But you're a shape-shifter, Kira," I said. She nodded.

"That means..."

"You are my daughter."

_Sebastian_

I was in shock. Kira was part alien? She looked surprised as well.

"My sister..she's still with the enemy. They were controlling us with CCNs."

CCNs are Complete Control Nano-chips. They only work on hybrids, and take complete control over the victim's body.

The Major was looking Kira in the eye. "Your real name isn't Kira. You are either Sakura or Akira, but your hair used to be blond. What happened?"

"Metaphen." Metaphen is a drug used to change a person's appearance.

"I'm coming to the moon base," Major Xerxes said.

_Kira_

Major Xerxes- my father- arrived two hours later. I was about to take Xi, a drug that would undo the effects of Metaphen. Hybrids are born with the ability to assume two forms- their hybrid form and their human form. Due to the Metaphen in my system, I was unable to assume either.

We were in the lab, on the fifth floor. I opened the bottle, and poured out a single, white pill. I swallowed it.

Pain flooded my body. I gripped the table tightly. Fortunately, the transformation was quick.

I could no longer stand. I started to cough up blood.

I fell to the floor, unconscious.

_Candace_

"No," Xerxes whispered. He held his daughter tightly. "Sakura."

"What's going on?" I asked.

"Sakura was born with a severe autoimmune disorder. If even a mild form of a virus enters her body, it could kill her. One virus paralyzed her from the waist down when she was only a few days old."

"We need to move her to a sterile room," Xander said.

Sebastian picked her up. "Where do I take her?"

"Down the hall, second room on the left."

Sebastian carried her, bridal style, to the clean room. He shut the door.

"There is a drug that can help," Xerxes said. "It's on my home planet. I can have it sent here, but it will take a few hours."

"Do we even _have _a few hours?" I asked.

Xander nodded. "I believe so."

Christopher ran up to us. "Where's Kira?" he demanded. "The Konaks are attacking the base!"

* * *

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	14. Secrets Arc: Preparations

**I hope some of you figured out what my pairings are!**

**I don't own Phineas and Ferb**

* * *

**Secrets Arc: Defense**

_Sebastian_

Kira, Xander and I attended Cascade High, a private school with a 56% Lithium agent student body. Candace, Jeremy, and Stacy transferred to Cascade at the beginning of the year.

Cascade had school uniforms for all of their students, which Stacy alternately liked and hated, depending on the day. Today, she loved the uniform.

"I mean, cream and lavender go together perfectly," she was saying (the girls wore cream vests and lavender skirts). Kira rolled her eyes.

"Are you guys busy this weekend?" she asked. "Because I'm supposed to go to the moon base on Saturday."

"We have a moon base?" I asked.

"You didn't know?"

We all shook our heads.

"Oh, well, it's mostly for shipbuilding and interplanetary negotiations."

_Candace_

We arrived at the moon base on Saturday morning. It looked like a tall, thin tower on top of a giant metal pod.

We met with Christopher, who was head of the base.

"What's wrong?" Kira asked.

"We intercepted a communication between General Liev and the Konak home world. He's requesting reinforcements."

"He's getting serious," Kira noted. "Do we have the materials to implement Plan Lambda347?"

"No."

Kira sighed. "I'll contact Marshal Xerxes." She turned to us. "Are you coming?"

* * *

**Please read and review!  
**


	15. Secrets Arc: Attack

**I don't own Phineas and Ferb**

* * *

**Secrets Arc: Attack**

_**Stacy**_

We jumped off our Ultacycles, summoning our Blades. Seconds later, the Droids attacked.

Droids are tiny black creatures, maybe two feet tall with claws for hands and crooked antennae, but they sure are vicious. They attack in groups, using dozens of Droids on a single target.

We were losing ground fast. We were seriously outnumbered.

_**Sakura**_

We rode across the darkened plain. I saw a swarm of Droids in the distance.

_They're not moving. Could they be attacking the others?_

They were. Sebastian and I jumped off our Ultacycles, summoned our Blades, and leapt into the fray.

It was soon obvious how poorly trained the others were. I mean, they're amazing with a photon gun, and they could fly a fighter pretty well, but they didn't know how to _connect _to their Blades, let the Blade dictate the flow of the battle.

I pointed my Blade at the sky. "Activate!" A shock wave rippled through the battlefield, making every Droid it touched vanish.

I passed out.

* * *

**One chapter left!**

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	16. Secrets Arc: Dreams

**I don't own Phineas and Ferb**

* * *

**Secrets Arc:**** Dreams  
****_Sakura_**

_I was on board a Konak command ship, but no one saw me. I heard voices._

_"Very...don't..."_

_I crept closer. General Liev was being scolded by a person hidden within the shadows._

_"Whatever you do, don't kill her. She's getting stronger. Soon the little flower will have fully bloomed, and my plan can be put into action."_

Little flower?

_Liev nodded. "I understand. Shall I proceed with our attack on Danville?"_

_"Of course."_

"Sakura! Sakura!"

**_Candace_**

We were trying to wake Sakura up. Suddenly, she bolted into a sitting position.

"Danville's in danger."

* * *

**That's the end of Part 1!  
Please read and review!**


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